Contacts of the helix formed by residues 70 - 84 (chain C) in PDB entry 2BHT
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 70 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C THR* 3.1 8.3 + - - -
69C SER* 1.3 80.1 - - - +
71C ASN* 1.3 66.2 + - - +
72C THR 3.5 1.1 - - - -
73C GLY* 3.7 2.3 + - - -
74C ILE* 3.4 25.8 + - - +
91C MET* 4.0 8.4 - - - -
99C ARG* 3.4 25.8 - - - +
103C MET* 4.4 4.1 - - - +
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Residues in contact with ASN 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C SER* 3.3 30.0 + - - +
41C LYS* 3.8 4.2 - - + +
42C ASP* 5.4 0.2 - - - +
68C THR* 4.0 0.2 + - - -
69C SER 4.0 0.6 - - - -
70C GLY* 1.3 75.2 - - - +
72C THR* 1.3 60.6 + - - +
74C ILE* 3.5 6.7 + - - +
75C ALA* 2.9 28.9 + - - +
99C ARG* 4.1 10.3 + - - +
280C CYS 5.7 0.2 - - - -
281C ASP* 2.9 27.6 + - - +
285C ARG* 2.8 27.4 + - - +
320C PLP 2.9 34.9 + - - +
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Residues in contact with THR 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LYS* 3.0 34.7 + - + +
44C ALA* 6.0 1.1 - - + -
45C ALA* 4.8 4.7 - - + +
48C MET* 4.6 12.3 - - + -
66C GLU* 5.0 1.1 - - + +
68C THR* 3.5 7.7 + - - -
71C ASN* 1.3 78.6 - - - +
73C GLY* 1.3 57.0 + - - +
75C ALA* 3.5 1.8 + - - +
76C LEU* 3.0 46.7 + - + +
140C GLN* 2.8 42.8 + - + +
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Residues in contact with GLY 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68C THR* 3.2 17.6 + - - -
70C GLY 3.7 0.4 + - - -
71C ASN 3.2 0.8 - - - -
72C THR* 1.3 73.9 - - - +
74C ILE* 1.3 55.4 + - - +
76C LEU* 3.0 4.3 + - - +
77C ALA* 2.8 34.1 + - - +
89C LEU* 3.3 36.7 - - - +
103C MET* 3.7 3.4 - - - -
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Residues in contact with ILE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ALA* 3.5 29.6 - - + +
70C GLY 3.4 16.3 + - - +
71C ASN* 3.6 8.7 - - - +
73C GLY* 1.3 73.0 - - - +
75C ALA* 1.3 63.6 - - - +
77C ALA* 3.4 5.3 + - - +
78C MET* 3.0 22.3 + - - +
99C ARG* 4.6 7.2 - - + +
102C ALA* 3.4 33.2 - - + -
103C MET* 3.4 13.8 - - + +
106C TYR* 3.8 16.2 - - + -
285C ARG* 3.3 36.6 - - - +
251D PHE* 6.5 0.4 - - + -
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Residues in contact with ALA 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ALA* 4.1 4.3 - - - -
41C LYS 3.9 11.4 - - - -
42C ASP* 3.6 21.3 - - - +
45C ALA* 3.5 22.9 - - + -
71C ASN 2.9 18.1 + - - +
72C THR 3.8 3.1 - - - +
74C ILE* 1.3 76.8 - - - +
76C LEU* 1.3 57.0 + - - +
78C MET* 2.8 30.9 - - + +
79C ILE* 2.9 13.9 + - - +
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Residues in contact with LEU 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ALA* 3.8 21.5 - - + +
48C MET* 4.7 2.0 - - + -
49C ILE* 3.6 20.7 - - + +
66C GLU* 4.3 15.3 - - + -
68C THR* 6.5 0.2 - - - -
72C THR* 3.0 36.1 + - + +
73C GLY* 3.0 6.5 + - - +
75C ALA* 1.3 74.3 - - - +
77C ALA* 1.3 56.0 + - - +
78C MET 3.1 1.1 - - - -
79C ILE* 3.9 1.5 - - - +
80C ALA* 2.5 38.8 + - - +
87C MET* 3.6 30.0 - - + +
89C LEU* 5.0 0.4 - - + -
138C LEU* 3.3 33.7 - - + -
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Residues in contact with ALA 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73C GLY 2.8 20.2 + - - +
74C ILE* 3.6 6.1 - - - +
76C LEU* 1.3 71.3 - - - +
78C MET* 1.3 50.1 + - - +
80C ALA* 3.2 3.0 + - - +
81C ALA* 2.5 36.7 + - - +
87C MET* 3.5 13.8 - - - +
103C MET* 3.9 12.1 - - - +
106C TYR* 3.3 30.1 - - + +
108C ALA* 3.9 13.2 - - + -
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Residues in contact with MET 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 4.4 4.9 - - + -
8C ILE* 5.0 3.4 - - + -
36C PRO* 3.8 29.8 - - + -
37C ALA* 3.9 9.2 - - + -
42C ASP* 3.9 15.0 - - + +
74C ILE 3.0 12.2 + - - +
75C ALA* 2.8 37.5 - - + +
77C ALA* 1.3 73.7 - - - +
79C ILE* 1.3 75.2 + - + +
81C ALA* 3.1 2.4 + - - +
82C LEU* 2.6 54.3 + - + +
106C TYR* 3.4 30.0 - - + +
249D GLY* 3.8 15.4 - - - +
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Residues in contact with ILE 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C ILE* 4.3 5.8 - - + -
42C ASP 4.8 0.2 - - - +
45C ALA* 4.4 2.9 - - + -
46C LEU* 3.3 53.2 - - + +
49C ILE* 3.3 27.8 - - + -
75C ALA 2.9 26.1 + - - +
76C LEU* 3.9 1.3 - - - +
78C MET* 1.3 87.5 - - + +
80C ALA* 1.3 57.7 + - - +
82C LEU* 3.3 14.3 - - + +
83C LYS* 3.0 53.3 + - + +
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Residues in contact with ALA 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ILE* 4.8 1.5 - - + +
76C LEU 2.5 23.1 + - - +
77C ALA* 3.3 4.5 - - - +
79C ILE* 1.3 71.8 - - - +
81C ALA* 1.3 59.5 + - - +
84C GLY* 3.0 24.6 + - - -
85C TYR* 3.3 39.2 + - + +
87C MET* 3.7 27.6 - - + -
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C ALA 2.5 20.9 + - - +
78C MET* 3.5 4.9 - - - +
80C ALA* 1.3 71.3 - - - +
82C LEU* 1.3 55.4 + - - +
83C LYS 3.3 0.7 + - - -
84C GLY* 4.4 0.9 + - - -
106C TYR 4.2 8.3 - - - +
18D ARG* 2.5 33.6 + - - -
245D ALA 3.2 27.4 - - - +
246D VAL 3.4 14.7 - - - +
247D ARG 3.5 3.8 - - - +
249D GLY* 3.5 9.9 - - - +
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Residues in contact with LEU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 3.7 24.5 - - + +
5C GLU* 3.8 45.4 - - + +
8C ILE* 6.1 0.9 - - + -
78C MET* 2.6 37.6 + - + +
79C ILE* 3.3 20.6 - - + +
81C ALA* 1.3 74.9 - - - +
83C LYS* 1.3 63.3 + - + +
18D ARG* 3.0 17.1 + - - +
248D GLU 3.4 25.1 - - - +
249D GLY* 4.6 0.2 - - - -
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Residues in contact with LYS 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C GLU* 3.4 25.6 + - - +
46C LEU* 4.5 4.7 - - - -
49C ILE* 3.7 24.7 - - + -
50C VAL* 4.0 17.1 - - - +
53C GLU* 4.2 18.6 + - - +
60C PRO* 4.1 15.3 - - + +
79C ILE* 3.0 37.4 + - + +
82C LEU* 1.3 86.0 - - + +
84C GLY* 1.3 60.3 + - - +
85C TYR* 4.2 15.5 - - + -
18D ARG* 3.7 10.3 + - - +
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Residues in contact with GLY 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C PRO* 3.4 5.0 - - - +
61C GLY* 2.7 33.8 + - - -
80C ALA 3.0 8.7 + - - -
81C ALA 4.4 1.1 + - - -
83C LYS* 1.3 82.3 - - - +
85C TYR* 1.3 58.3 - - - +
18D ARG* 4.3 5.1 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il